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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cBioPortalData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cBioPortalData_2.21.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/cBioPortalData.Rcheck’
* using R version 4.5.0 Patched (2025-04-21 r88169)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cBioPortalData/DESCRIPTION’ ... OK
* this is package ‘cBioPortalData’ version ‘2.21.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cBioPortalData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.portalExperiments: no visible binding for global variable
  ‘molecularAlterationType’
.portalExperiments: no visible binding for global variable ‘datatype’
fetchData: no visible binding for global variable
  ‘molecularAlterationType’
fetchData: no visible binding for global variable ‘datatype’
Undefined global functions or variables:
  datatype molecularAlterationType
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘cBioPortalData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cBioCache-defunct
> ### Title: Defunct cache helper functions
> ### Aliases: cBioCache-defunct removeDataCache
> 
> ### ** Examples
> 
> 
> cbio <- cBioPortal()
> 
> cBioPortalData(
+     cbio, by = "hugoGeneSymbol",
+     studyId = "acc_tcga",
+     genePanelId = "AmpliSeq",
+     molecularProfileIds =
+         c("acc_tcga_rppa", "acc_tcga_linear_CNA", "acc_tcga_mutations")
+ )
harmonizing input:
  removing 1 colData rownames not in sampleMap 'primary'
A MultiAssayExperiment object of 3 listed
 experiments with user-defined names and respective classes.
 Containing an ExperimentList class object of length 3:
 [1] acc_tcga_mutations: RangedSummarizedExperiment with 25 rows and 20 columns
 [2] acc_tcga_linear_CNA: SummarizedExperiment with 8 rows and 90 columns
 [3] acc_tcga_rppa: SummarizedExperiment with 1 rows and 46 columns
Functionality:
 experiments() - obtain the ExperimentList instance
 colData() - the primary/phenotype DataFrame
 sampleMap() - the sample coordination DataFrame
 `$`, `[`, `[[` - extract colData columns, subset, or experiment
 *Format() - convert into a long or wide DataFrame
 assays() - convert ExperimentList to a SimpleList of matrices
 exportClass() - save data to flat files
> 
> removeDataCache(
+     cbio, by = "hugoGeneSymbol",
+     studyId = "acc_tcga",
+     genePanelId = "AmpliSeq",
+     molecularProfileIds =
+         c("acc_tcga_rppa", "acc_tcga_linear_CNA", "acc_tcga_mutations"),
+     dry.run = TRUE
+ )
Error in lifeCycle(package = "cBioPortalData", title = "cBioCache", cycle = "defunct") : 
  'removeDataCache' is defunct.
  See help('cBioCache-defunct').
Calls: removeDataCache -> lifeCycle -> do.call -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/cBioPortalData.Rcheck/00check.log’
for details.